3S3S | pdb_00003s3s

Transglutaminase 2 in complex with a novel inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3S3S/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-18 Released: 2012-06-06 
• Deposition Author(s): Lindemann, I., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.296 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Inhibitors of Transglutaminase 2: A therapeutic option in celiac disease

Lindemann, I., Boettcher, J., Oertel, K., Weber, J., Hils, M., Pasternack, R., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.55 kDa 
• Atom Count: 5,013 
• Modeled Residue Count: 625 
• Deposited Residue Count: 699 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-glutamine gamma-glutamyltransferase 2	A	694	Homo sapiens	Mutation(s): 0  Gene Names: TGM2 EC: 2.3.2.13 (PDB Primary Data), 2.3.1 (UniProt), 3.4 (UniProt), 3.5.1.44 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21980 (Homo sapiens) Explore P21980  Go to UniProtKB:  P21980
PHAROS:  P21980 GTEx:  ENSG00000198959

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide inhibitor	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
XW1	B	L-PEPTIDE LINKING	C9 H17 N O4		ALA

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000937	B	N-[(2R)-2-{[(benzyloxy)carbonyl]amino}-7-ethoxy-7-oxoheptanoyl]-L-valyl-L-prolyl-L-leucine	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.296 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.439	α = 90
b = 71.439	β = 90
c = 310.34	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Lindemann, I., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection